Evolutionary Genetics: Part 0.2 Introduction to Population genetics

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1 Evolutionary Genetics: Part 0.2 Introduction to Population genetics S. chilense S. peruvianum Winter Semester Prof Aurélien Tellier FG Populationsgenetik

2 Population genetics Evolution = changes between generations of frequency of characters, traits or alleles Why study the genetics of populations? the population is the main unit at which selection acts!!!!!!!!!

3 Population genetics Populations and species show variability: what type and how much genetic variation exist within populations/species? what are the forces that influence the amount of variation within populations?

4 Population genetics: 4 evolutionary forces random genomic processes (mutation, duplication, recombination, gene conversion) natural selection molecular diversity random spatial process (migration) random demographic process (drift) Population genetics investigates the laws governing the genetic structure of populations, and changes in allele frequencies over time

5 Population genetics: 4 evolutionary forces random genomic processes (mutation, duplication, recombination, gene conversion) molecular diversity natural selection phenotypic variability random spatial process (migration) random demographic process (drift) We want to infer the role of the evolutionary forces from sequence data (very useful tool is the coalescent theory)

6 Population genetics Populations and species show variability: what type and how much genetic variation exist within populations/species? what are the forces that influence the amount of variation within populations? how can population genetics principles be used to address questions in human health, environmental issues, and evolution?

7 Population genetics: applications Examples and case studies of population genetics applications E1: Study of Biodiversity E2: Conservation genetics E3: Interactions host-parasites E4: Genetic exchanges between species E5: Genetic exchanges between populations E6: Genetic barriers E7: Genetic exchanges between individuals E8: Legal medicine E9: Gene evolution E10: Localization of genes E11: Understanding mechanisms of adaptation E12: Reveal the demographic history of species

8 E1: Study of Biodiversity Counting species Characterizing the genetic diversity of endangered species in relation to group/population sizes, inbreeding Ex. Cheetah in Namibia, Elephants, Northern Spotted owls, Grizzli bears,

9 E2: Conservation genetics Conservation genetics and reserve of genetic resources Animal breeding (Oysters), Fish farms (salmon, trouts) Newly re-introduced species (Alpine Ibex and Lynx in the Alps)

10 E2: Conservation genetics Conservation genetics and reserve of genetic resources Banks for seeds of endangered plant species Determine and assess the genetic diversity of crop ancestors => preserve source of new characters for crop improvements

11 E3: Interactions host-parasites Correlation between host and parasite genetic diversity Adaptation of parasites to hosts, how fast do parasites adapt? Transmission of resistance factors between strains (esp. antibiotics) Selection in virus (HIV) or bacteria during multiplication in hosts

12 E3: Interactions host-parasites Evolution of human/animal parasites Tanabe et al. 2010: Origin and population structure of Plasmodium falciparum (malaria)

13 E3: Interactions host-parasites Evolution of human/animal parasites Yalcindag et al. 2012: Origin and population structure of Plasmodium falciparum in South-America

14 E3: Interactions host-parasites Examples of plant-parasite coevolution Stuckenbrock et al. 2011, Evolution of Mycosphaerella graminicola pathogen of wheat

15 E3: Interactions host-parasites Examples of new emergent diseases on animals and plants

16 E4: Gene flow between species Study the existence of hybrid species (often in plants) Hybrid zones: for house mice (Mus musculus) Bonhomme et al. 2007

17 E4: Gene flow between species Horizontal gene transfer from one species to another: ex of virulence factors in parasite to favor host-jump Gardiner et al. 2012: horizontal gene transfer between fungal pathogens on wheat and barley

18 E5: Gene flow between populations Understand migration between populations, migration flow between human populations Reconstructing the history of colonization of new environment Reassign people to populations (recent migrants) Alves et al Admixture between Neanderthals and recent hominids?

19 E6: Barriers to gene flow Reveal genetic barriers between species or sub-species (important in conservation) Behavioral barriers (mating avoidance, ) Cultural or social

20 E7: Genetic exchanges between individuals Choice of partner is this choice random? Studies show that in human, mice, fish, individuals prefer complimentary individuals for their HLA/MHC system Inbreeding Tests for genetic diseases Charles II inbreeding coefficient = 0.254

21 E8: Legal medicine Genetic prints identification of suspects

22 E9: Gene evolution More examples will come later Intraspecific Estimation of divergence between populations Interspecific Divergence time between species Marko and Hart Trends Evol 2011 Molecular Taxonomy Intergenic divergence between duplicated genes rates of gene conversion Wheeler et al. PNAS 2001

23 E10: Gene localization Find genes for human diseases linkage analysis in a family linkage disequilibrium mapping Genome wide association studies (GWAs) Quantitative traits loci (QTLs)

24 E11: Mechanisms of adaptation Reveal mechanisms of adaptation clines in frequency of alleles selection at HLA/MHC alleles speciation processes: which mutations are involved?

25 E12: Demographic history of species Demographic expansions, Demographic bottlenecks Domestication of plants or animals (apples, wheat, maize, ) Expansion of viral or bacterial strains Effect of climatic changes on population sizes Mechanisms of colonization from a glacial refugia